after thinking about it why did he have to be Khan. why not one of the other supermen that were frozen? when admiral marcus boarded the botany bay why not open a different cryo tube then the one containing Khan? Say the one containing Khans 1st officer John Harrison, who is just as loyal to Khans cause. you could have had that nod to TWOK and space seed but have your own new villain.

For the same reason you don't make a Batman film with a sociopath clown and call him Bozo.

why not if it works. if Bozo is an outstanding villian as was John Harrison it would be fine.

Well, in the case of Batman, there's better marketing potential if the villain is the Joker than if he's Bozo.

It's a fine enough argument for using Khan, except since they kept him a secret they couldn't take advantage of any marketing potential the character would have had.